SEA-PHAGES | PCR Primers

Link to this post \| posted 02 Mar, 2016 16:12
saleadon	Hi Everyone, In "Exploring Bacteriophage Biology", one suggested bioinformatics experiment is to design cluster-specific DNA primers. The article mentions that there is a list of existing primers on phagesdb.org under “Phorum”. However, I can't find that. Has it been moved or deleted? Thanks, Steve

Link to this post \| posted 03 Mar, 2016 16:05
DanRussell	saleadon Hi Everyone, In "Exploring Bacteriophage Biology", one suggested bioinformatics experiment is to design cluster-specific DNA primers. The article mentions that there is a list of existing primers on phagesdb.org under “Phorum”. However, I can't find that. Has it been moved or deleted? Thanks, Steve Hi Steve, That document needs to be updated! Yes, the PhagesDB Phorum has indeed been deleted. And I'm not sure that we'd necessarily recommend that particular experiment either, since it has proved of limited use. It might be an interesting teaching/thought experiment…like: can you locate regions that are conserved in all the members of a subcluster? A cluster? Or not? (i.e., Is it even possible to design cluster-specific primers?) In any event, I know that Alex Peister at Morehouse College has been the de facto go-to person for cluster primers, so she would be a good resource if you're interested in the current state of those attempts. –Dan

Link to this post | posted 03 Mar, 2016 16:05

DanRussell

saleadon
Hi Everyone,
In "Exploring Bacteriophage Biology", one suggested bioinformatics experiment is to design cluster-specific DNA primers. The article mentions that there is a list of existing primers on phagesdb.org under “Phorum”. However, I can't find that. Has it been moved or deleted?
Thanks,
Steve

Hi Steve,

That document needs to be updated! Yes, the PhagesDB Phorum has indeed been deleted. And I'm not sure that we'd necessarily recommend that particular experiment either, since it has proved of limited use. It might be an interesting teaching/thought experiment…like: can you locate regions that are conserved in all the members of a subcluster? A cluster? Or not? (i.e., Is it even possible to design cluster-specific primers?)

In any event, I know that Alex Peister at Morehouse College has been the de facto go-to person for cluster primers, so she would be a good resource if you're interested in the current state of those attempts.

–Dan

Link to this post \| posted 03 Mar, 2016 21:35
saleadon	Dan Russell saleadon Hi Everyone, In "Exploring Bacteriophage Biology", one suggested bioinformatics experiment is to design cluster-specific DNA primers. The article mentions that there is a list of existing primers on phagesdb.org under “Phorum”. However, I can't find that. Has it been moved or deleted? Thanks, Steve Hi Steve, That document needs to be updated! Yes, the PhagesDB Phorum has indeed been deleted. And I'm not sure that we'd necessarily recommend that particular experiment either, since it has proved of limited use. It might be an interesting teaching/thought experiment…like: can you locate regions that are conserved in all the members of a subcluster? A cluster? Or not? (i.e., Is it even possible to design cluster-specific primers?) In any event, I know that Alex Peister at Morehouse College has been the de facto go-to person for cluster primers, so she would be a good resource if you're interested in the current state of those attempts. –Dan Thanks Dan. After looking in the literature, it appeared that this would not be a trivial project. I appreciate the information.

Link to this post | posted 03 Mar, 2016 21:35

saleadon

Dan Russell
saleadon
Hi Everyone,
In "Exploring Bacteriophage Biology", one suggested bioinformatics experiment is to design cluster-specific DNA primers. The article mentions that there is a list of existing primers on phagesdb.org under “Phorum”. However, I can't find that. Has it been moved or deleted?
Thanks,
Steve

Hi Steve,

That document needs to be updated! Yes, the PhagesDB Phorum has indeed been deleted. And I'm not sure that we'd necessarily recommend that particular experiment either, since it has proved of limited use. It might be an interesting teaching/thought experiment…like: can you locate regions that are conserved in all the members of a subcluster? A cluster? Or not? (i.e., Is it even possible to design cluster-specific primers?)

In any event, I know that Alex Peister at Morehouse College has been the de facto go-to person for cluster primers, so she would be a good resource if you're interested in the current state of those attempts.

–Dan

Thanks Dan. After looking in the literature, it appeared that this would not be a trivial project. I appreciate the information.

Link to this post \| posted 27 Sep, 2019 05:14
debbie	Hi all, Recently Krista Freeman, a post doc in the Hatfull lab, and Julia Kovalski, an undergrad designed primers for 60 cluster/subclusters of mycobacteriophages. These primers were designed for verification of phage lysates in the Hatfull lab (and not to prematurely assign cluster designations to unsequenced phages). Attached is an Excel sheet of the primers/phages. Krista thought having the fasta files of the phages would be helpful. I thought adding a picture of Julia and Krista would be fun! Edited 27 Sep, 2019 05:15 27Kb 2.80Mb 1.17Mb

Link to this post | posted 27 Sep, 2019 05:14

debbie

Hi all,
Recently Krista Freeman, a post doc in the Hatfull lab, and Julia Kovalski, an undergrad designed primers for 60 cluster/subclusters of mycobacteriophages. These primers were designed for verification of phage lysates in the Hatfull lab (and not to prematurely assign cluster designations to unsequenced phages). Attached is an Excel sheet of the primers/phages. Krista thought having the fasta files of the phages would be helpful. I thought adding a picture of Julia and Krista would be fun!

Edited 27 Sep, 2019 05:15

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